Over the past 30 years, the amount of DNA sequence information that has been generated and deposited into Genbank has grown exponentially. Many of the next-generation sequencing technologies use a form of sequencing by synthesis (SBS), wherein specially designed nucleotides and DNA polymerases are used to read the sequence of single-stranded DNA templates in a controlled manner. Pyrosequencing is a form of SBS which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Rotherberg et al. teach the use of large arrays of chemically sensitive FETs (chemFETs) or more specifically ISFETs for monitoring reactions, including for example nucleic acid (e.g., DNA) sequencing reactions, based on monitoring analytes present, generated or used during a reaction. See U.S. Patent Application Publication No. 20100137143, hereby incorporated by reference. More generally, arrays including large arrays of chemFETs may be employed to detect and measure static and/or dynamic amounts or concentrations of a variety of analytes (e.g., hydrogen ions, other ions, non-ionic molecules or compounds, etc.). Rotherberg et al. teach the measurement of hydrogen ions, rather than the pyrophosphate normally measured in pyrosequencing.
However, there are types of sequences which are difficult to sequence (even with these newer approaches), and in particular, sequences that contain consecutive repeats of a particular base. What is needed is an improved method which addresses the ability to sequence all types of sequence.